|
1
|
Ishimoto U, Kondo S, Ohba A, Sasaki M,
Sakamoto Y, Morizane C, Ueno H and Okusaka T: Prognostic factors
for survival in patients with advanced intrahepatic
cholangiocarcinoma treated with gemcitabine plus cisplatin as
first-line treatment. Oncology. 94:72–78. 2018.PubMed/NCBI View Article : Google Scholar
|
|
2
|
Jia Y and Xie J: Promising molecular
mechanisms responsible for gemcitabine resistance in cancer. Genes
Dis. 2:299–306. 2015.PubMed/NCBI View Article : Google Scholar
|
|
3
|
Clough E and Barrett T: The gene
expression omnibus database. Methods Mol Biol. 1418:93–110.
2016.PubMed/NCBI View Article : Google Scholar
|
|
4
|
Xiao X, Wan Z, Liu X, Chen H, Zhao X, Ding
R, Cao Y, Zhou F, Qiu E, Liang W, et al: Screening of therapeutic
targets for pancreatic cancer by bioinformatics methods. Horm Metab
Res. 55:420–425. 2023.PubMed/NCBI View Article : Google Scholar
|
|
5
|
Shen P, He X, Lan L, Hong Y and Lin M:
Identification of cell division cycle 20 as a candidate biomarker
and potential therapeutic target in bladder cancer using
bioinformatics analysis. Biosci Rep. 40(BSR20194429)2020.PubMed/NCBI View Article : Google Scholar
|
|
6
|
Liu X, Jia Y, Shi C, Kong D, Wu Y, Zhang
T, Wei A and Wang D: CYP4B1 is a prognostic biomarker and potential
therapeutic target in lung adenocarcinoma. PLoS One.
16(e0247020)2021.PubMed/NCBI View Article : Google Scholar
|
|
7
|
Sungwan P, Lert-Itthiporn W, Silsirivanit
A, Klinhom-On N, Okada S, Wongkham S and Seubwai W: Bioinformatics
analysis identified CDC20 as a potential drug target for
cholangiocarcinoma. PeerJ. 9(e11067)2021.PubMed/NCBI View Article : Google Scholar
|
|
8
|
Xiao C, Yin X, Xi R, Yuan C and Ou Y:
Molecular mechanisms of reversal of multidrug resistance in breast
cancer by inhibition of P-gp by cytisine N-isoflavones derivatives
explored through network pharmacology, molecular docking, and
molecular dynamics. Int J Mol Sci. 26(3813)2025.PubMed/NCBI View Article : Google Scholar
|
|
9
|
Zhang N, Tian X, Liu F, Jin X, Zhang J,
Hao L, Jiang S and Liu Q: Reversal of sorafenib resistance in
hepatocellular carcinoma by curcumol: Insights from network
pharmacology, molecular docking, and experimental validation. Front
Pharmacol. 16(1514997)2025.PubMed/NCBI View Article : Google Scholar
|
|
10
|
Sripa B, Seubwai W, Vaeteewoottacharn K,
Sawanyawisuth K, Silsirivanit A, Kaewkong W, Muisuk K, Dana P,
Phoomak C, Lert-Itthiporn W, et al: Functional and genetic
characterization of three cell lines derived from a single tumor of
an Opisthorchis viverrini-associated cholangiocarcinoma patient.
Hum Cell. 33:695–708. 2020.PubMed/NCBI View Article : Google Scholar
|
|
11
|
Sripa B, Leungwattanawanit S, Nitta T,
Wongkham C, Bhudhisawasdi V, Puapairoj A, Sripa C and Miwa M:
Establishment and characterization of an opisthorchiasis-associated
cholangiocarcinoma cell line (KKU-100). World J Gastroenterol.
11:3392–3397. 2005.PubMed/NCBI View Article : Google Scholar
|
|
12
|
Kidoikhammouan S, Lert-Itthiporn W,
Deenonpoe R, Saengboonmee C, Obchoei S, Wongkham S and Seubwai W:
Targeting EGFR activation to overcome gemcitabine resistance in
cholangiocarcinoma. Anticancer Res. 44:5393–5404. 2024.PubMed/NCBI View Article : Google Scholar
|
|
13
|
Varamo C, Peraldo-Neia C, Ostano P,
Basiricò M, Raggi C, Bernabei P, Venesio T, Berrino E, Aglietta M,
Leone F and Cavalloni G: Establishment and characterization of a
new intrahepatic cholangiocarcinoma cell line resistant to
gemcitabine. Cancers (Basel). 11(519)2019.PubMed/NCBI View Article : Google Scholar
|
|
14
|
Vergara-Gómez L, Bizama C, Zhong J,
Buchegger K, Suárez F, Rosa L, Ili C, Weber H, Obreque J, Espinoza
K, et al: A novel gemcitabine-resistant gallbladder cancer model
provides insights into molecular changes occurring during acquired
resistance. Int J Mol Sci. 24(7238)2023.PubMed/NCBI View Article : Google Scholar
|
|
15
|
Zhou J, Zhang L, Zheng H, Ge W, Huang Y,
Yan Y, Zhou X, Zhu W, Kong Y, Ding Y and Wang W: Identification of
chemoresistance-related mRNAs based on gemcitabine-resistant
pancreatic cancer cell lines. Cancer Med. 9:1115–1130.
2020.PubMed/NCBI View Article : Google Scholar
|
|
16
|
Chaisaingmongkol J, Budhu A, Dang H,
Rabibhadana S, Pupacdi B, Kwon SM, Forgues M, Pomyen Y,
Bhudhisawasdi V, Lertprasertsuke N, et al: Common molecular
subtypes among Asian hepatocellular carcinoma and
cholangiocarcinoma. Cancer Cell. 32:57–70.e3. 2017.PubMed/NCBI View Article : Google Scholar
|
|
17
|
Galaxy Community: The Galaxy platform for
accessible, reproducible, and collaborative data analyses: 2024
Update. Nucleic Acids Res. 52 (W1):W83–W94. 2024.PubMed/NCBI View Article : Google Scholar
|
|
18
|
Bardou P, Mariette J, Escudié F, Djemiel C
and Klopp C: jvenn: An interactive Venn diagram viewer. BMC
Bioinformatics. 15(293)2014.PubMed/NCBI View Article : Google Scholar
|
|
19
|
Cerami E, Gao J, Dogrusoz U, Gross BE,
Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, et
al: The cBio cancer genomics portal: An open platform for exploring
multidimensional cancer genomics data. Cancer Discov. 2:401–404.
2012.PubMed/NCBI View Article : Google Scholar
|
|
20
|
Livak KJ and Schmittgen TD: Analysis of
relative gene expression data using real-time quantitative PCR and
the 2(-Delta Delta C(T)) method. Methods. 25:402–408.
2001.PubMed/NCBI View Article : Google Scholar
|
|
21
|
Abramson J, Adler J, Dunger J, Evans R,
Green T, Pritzel A, Ronneberger O, Willmore L, Ballard AJ, Bambrick
J, et al: Accurate structure prediction of biomolecular
interactions with AlphaFold 3. Nature. 630:493–500. 2024.PubMed/NCBI View Article : Google Scholar
|
|
22
|
Jurrus E, Engel D, Star K, Monson K,
Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, et al:
Improvements to the APBS biomolecular solvation software suite.
Protein Sci. 27:112–128. 2018.PubMed/NCBI View
Article : Google Scholar
|
|
23
|
Søndergaard CR, Olsson MHM, Rostkowski M
and Jensen JH: Improved treatment of ligands and coupling effects
in empirical calculation and rationalization of pKa values. J Chem
Theory Comput. 7:2284–2295. 2011.PubMed/NCBI View Article : Google Scholar
|
|
24
|
Tian C, Kasavajhala K, Belfon KAA,
Raguette L, Huang H, Migues AN, Bickel J, Wang Y, Pincay J, Wu Q
and Simmerling C: ff19SB: Amino-acid-specific protein backbone
parameters trained against quantum mechanics energy surfaces in
solution. J Chem Theory Comput. 16:528–552. 2020.PubMed/NCBI View Article : Google Scholar
|
|
25
|
Jorgensen WL, Chandrasekhar J, Madura JD,
Impey RW and Klein ML: Comparison of simple potential functions for
simulating liquid water. J Chem Phys. 79:926–935. 1983.
|
|
26
|
Wang S, Xie J, Pei J and Lai L: CavityPlus
2022 update: An integrated platform for comprehensive protein
cavity detection and property analyses with user-friendly tools and
cavity databases. J Mol Biol. 435(168141)2023.PubMed/NCBI View Article : Google Scholar
|
|
27
|
Xu Y, Wang S, Hu Q, Gao S, Ma X, Zhang W,
Shen Y, Chen F, Lai L and Pei J: CavityPlus: A web server for
protein cavity detection with pharmacophore modelling, allosteric
site identification and covalent ligand binding ability prediction.
Nucleic Acids Res. 46 (W1):W374–W379. 2018.PubMed/NCBI View Article : Google Scholar
|
|
28
|
Eberhardt J, Santos-Martins D, Tillack AF
and Forli S: AutoDock Vina 1.2.0: New docking methods, expanded
force field, and python bindings. J Chem Inf Model. 61:3891–3898.
2021.PubMed/NCBI View Article : Google Scholar
|
|
29
|
Trott O and Olson AJ: AutoDock Vina:
Improving the speed and accuracy of docking with a new scoring
function, efficient optimization, and multithreading. J Comput
Chem. 31:455–461. 2010.PubMed/NCBI View Article : Google Scholar
|
|
30
|
Wei W, Chen H and Liu S: Knockdown of
Rhotekin 2 expression suppresses proliferation and invasion and
induces apoptosis in hepatocellular carcinoma cells. Mol Med Rep.
13:4865–4871. 2016.PubMed/NCBI View Article : Google Scholar
|
|
31
|
Pang X, Li R, Shi D, Pan X, Ma C, Zhang G,
Mu C and Chen W: Knockdown of Rhotekin 2 expression suppresses
proliferation and induces apoptosis in colon cancer cells. Oncol
Lett. 14:8028–8034. 2017.PubMed/NCBI View Article : Google Scholar
|
|
32
|
Wang X, Zhang L, Wang W and Wang Y, Chen
Y, Xie R, Li X and Wang Y: Rhotekin 2 silencing inhibits
proliferation and induces apoptosis in human osteosarcoma cells.
Biosci Rep. 38(BSR20181384)2018.PubMed/NCBI View Article : Google Scholar
|
|
33
|
Ji L and Huang Y, Zhang Y, Peng A, Qin J,
Lu S and Huang Y: RTKN2 is associated with unfavorable prognosis
and promotes progression in non-small-cell lung cancer. Onco
Targets Ther. 13:10729–10738. 2020.PubMed/NCBI View Article : Google Scholar
|
|
34
|
Collier FM, Loving A, Baker AJ, McLeod J,
Walder K and Kirkland MA: RTKN2 induces NF-kappaB dependent
resistance to intrinsic apoptosis in HEK cells and regulates BCL-2
genes in human CD4(+) lymphocytes. J Cell Death. 2:9–23.
2009.PubMed/NCBI View Article : Google Scholar
|
|
35
|
Zhang X, Wang J and Li H: RTKN2 knockdown
alleviates the malignancy of breast cancer cells by regulating the
Wnt/β-catenin pathway. Sci Rep. 13(23023)2023.PubMed/NCBI View Article : Google Scholar
|
|
36
|
Zhang GF, Qiu L, Yang SL, Wu JC and Liu
TJ: Wnt/β-catenin signaling as an emerging potential key
pharmacological target in cholangiocarcinoma. Biosci Rep.
40(BSR20193353)2020.PubMed/NCBI View Article : Google Scholar
|
|
37
|
Liu C, Jin Y and Fan Z: The mechanism of
warburg effect-induced chemoresistance in cancer. Front Oncol.
11(698023)2021.PubMed/NCBI View Article : Google Scholar
|
|
38
|
Bhattacharya B, Mohd Omar MF and Soong R:
The Warburg effect and drug resistance. Br J Pharmacol.
173:970–979. 2016.PubMed/NCBI View Article : Google Scholar
|
|
39
|
de Oliveira Santos LAB and de Aragão
Batista MV: Structure-based virtual screening and drug repurposing
studies indicate potential inhibitors of bovine papillomavirus E6
oncoprotein. Microbiol Immunol. 68:414–426. 2024.PubMed/NCBI View Article : Google Scholar
|
|
40
|
Soldi R, Halder TG, Sampson S,
Vankayalapati H, Weston A, Thode T, Bhalla KN, Ng S, Rodriguez Del
Villar R, Drenner K, et al: The small molecule BC-2059 inhibits
wingless/integrated (Wnt)-dependent gene transcription in cancer
through disruption of the transducin β-Like 1-β-catenin protein
complex. J Pharmacol Exp Ther. 378:77–86. 2021.PubMed/NCBI View Article : Google Scholar
|
|
41
|
Nomura M, Rainusso N, Lee YC, Dawson B,
Coarfa C, Han R, Larson JL, Shuck R, Kurenbekova L and Yustein JT:
Tegavivint and the β-catenin/ALDH axis in chemotherapy-resistant
and metastatic osteosarcoma. J Natl Cancer Inst. 111:1216–1227.
2019.PubMed/NCBI View Article : Google Scholar
|
|
42
|
Savvidou I, Khong T, Cuddihy A, McLean C,
Horrigan S and Spencer A: β-Catenin inhibitor BC2059 is efficacious
as monotherapy or in combination with proteasome inhibitor
bortezomib in multiple myeloma. Mol Cancer Ther. 16:1765–1778.
2017.
|
|
43
|
Fowler NH, Samaniego F, Jurczak W, Ghosh
N, Derenzini E, Reeves JA, Knopińska-Posłuszny W, Cheah CY,
Phillips T, Lech-Maranda E, et al: Umbralisib, a dual PI3Kδ/CK1ε
inhibitor in patients with relapsed or refractory indolent
lymphoma. J Clin Oncol. 39:1609–1618. 2021.
|
|
44
|
Dhillon S and Keam SJ: Umbralisib: First
approval. Drugs. 81:857–866. 2021.PubMed/NCBI View Article : Google Scholar
|
|
45
|
Gough SM, Flanagan JJ, Teh J, Andreoli M,
Rousseau E, Pannone M, Bookbinder M, Willard R, Davenport K,
Bortolon E, et al: Oral estrogen receptor PROTAC vepdegestrant
(ARV-471) is highly efficacious as monotherapy and in combination
with CDK4/6 or PI3K/mTOR pathway inhibitors in preclinical ER+
breast cancer models. Clin Cancer Res. 30:3549–3563.
2024.PubMed/NCBI View Article : Google Scholar
|
|
46
|
Campone M, De Laurentiis M, Jhaveri K, Hu
X, Ladoire S, Patsouris A, Zamagni C, Cui J, Cazzaniga M, Cil T, et
al: Vepdegestrant, a PROTAC estrogen receptor degrader, in advanced
breast cancer. N Engl J Med. 393:556–568. 2025.PubMed/NCBI View Article : Google Scholar
|
|
47
|
Hamilton EP, Ma C, De Laurentiis M, Iwata
H, Hurvitz SA, Wander SA, Danso M, Lu DR, Perkins Smith J, Liu Y,
et al: VERITAC-2: A phase III study of vepdegestrant, a PROTAC ER
degrader, versus fulvestrant in ER+/HER2-advanced breast cancer.
Future Oncol. 20:2447–2455. 2024.PubMed/NCBI View Article : Google Scholar
|
|
48
|
Hurvitz S, Schott A, Ma C, Nanda R, Zahrah
G, Hunter N, Tan A, Telli M, Mesias JA, Jeselsohn R, et al:
Abstract PO3-05-08: Updated results from VERITAC evaluating
vepdegestrant, a PROteolysis targeting chimera (PROTAC) estrogen
receptor (ER) degrader, in ER-positive/human epidermal growth
factor receptor 2 (HER2)-negative advanced breast cancer. Cancer
Res. 84 (9 Suppl)(PO3-05-08)2024.
|
|
49
|
Iwata H, Hamilton E, Ma C, De Laurentiis
M, Hurvitz SA, Wander SA, Danso MA, Lu DR, Perkins J, Liu Y, et al:
73TiP global phase III studies evaluating vepdegestrant in estrogen
receptor (ER)+/human epidermal growth factor receptor 2
(HER2)-advanced breast cancer: VERITAC-2 and VERITAC-3. Ann Oncol.
34 (Suppl 4)(S1493)2023.
|
|
50
|
Hewitt DJ, Aurora SK, Dodick DW, Goadsby
PJ, Ge YJ, Bachman R, Taraborelli D, Fan X, Assaid C, Lines C and
Ho TW: Randomized controlled trial of the CGRP receptor antagonist
MK-3207 in the acute treatment of migraine. Cephalalgia.
31:712–722. 2011.PubMed/NCBI View Article : Google Scholar
|